\documentclass{article}

\usepackage{float}

\usepackage[table]{xcolor} %supports coloring single cells in a table
\usepackage{longtable} %gives multi-page tables
%the following didn't really work, but it did happen to fix the issue :shrug:
%https://tex.stackexchange.com/questions/287283/how-to-define-caption-width-in-longtable
\setlength{\LTcapwidth}{\textwidth}

\usepackage{makecell}

\usepackage{hhline}
\usepackage{hyperref}

\usepackage[margin=1in]{geometry}
\usepackage{pdflscape}
%\usepackage{url}
%\usepackage{caption}

%https://tex.stackexchange.com/questions/98388/how-to-make-table-with-rotated-table-headers-in-latex
\usepackage{adjustbox}
\usepackage{array}
\usepackage{booktabs}
\usepackage{multirow}
\newcolumntype{R}[2]{ 
    >{\adjustbox{angle=#1,lap=\width-(#2)}\bgroup}%
    c%
    <{\egroup}%
}
\newcommand*\rot{\multicolumn{1}{R{90}{1em}|}}% no optional argument here, please!
\newcommand*\rotf{\multicolumn{1}{|R{90}{1em}|}}% no optional argument here, please!
\newcommand*\rotd{\multicolumn{1}{R{90}{1em}||}}

\newcommand*{\ttrow}{
  \global\let\rowfont\ttfamily
  \ttfamily
}
\newcommand*{\unttrow}{
  \global\let\rowfont\relax
  \mdseries
}
\newcommand*{\rowfont}{}

%used for creating code blocks for the command line invocations
\usepackage{listings}
\lstset{basicstyle=\ttfamily,
  showstringspaces=false,
  commentstyle=\color{red},
  %keywordstyle=\color{blue}
}

\begin{document}

\title{Supplemental Document}
\author{J. Matthew Holt et al.}

\maketitle
\tableofcontents

\newpage
\input{{"{"}}{{ PREFIX+'_tex/metadata_template.tex' }}}

\newpage
\input{{"{"}}{{ PREFIX+'_tex/pipeline_template.tex' }}}

\newpage
\input{{"{"}}{{ PREFIX+'_tex/training_template.tex' }}}

{% for aligner in ALIGNER_ORDER %}
    {% for caller in sorted(PARSED_DATA[aligner].keys()) %}
        \newpage
        \input{{"{"}}{{ '{prefix}_tex/full_results_{aligner}_{caller}.tex'.format(prefix=PREFIX, aligner=aligner, caller=caller) }}}
    {% endfor %}
{% endfor %}

\newpage
\input{{"{"}}{{ PREFIX+'_tex/hardcoded_template.tex' }}}

%\input{{"{"}}{{ PREFIX+'_tex/metadata_outline.tex' }}}

%\input{{"{"}}{{ PREFIX+'_tex/rtg_compare.tex' }}}

%\input{{"{"}}{{ PREFIX+'_tex/truvari_compare.tex' }}}

\end{document}
